[English] 日本語
Yorodumi
- PDB-4d64: Structure of porin Omp-Pst1 from P. stuartii; the crystallographi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d64
TitleStructure of porin Omp-Pst1 from P. stuartii; the crystallographic symmetry generates a dimer of trimers.
ComponentsPORIN 1
KeywordsTRANSPORT PROTEIN / BACTERIAL JUNCTION / STERIC-ZIPPER / DIMER OF TRIMERS
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin ...Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesPROVIDENCIA STUARTII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsNasrallah, C. / Colletier, J.P.
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Porin self-association enables cell-to-cell contact inProvidencia stuartiifloating communities.
Authors: El-Khatib, M. / Nasrallah, C. / Lopes, J. / Tran, Q.T. / Tetreau, G. / Basbous, H. / Fenel, D. / Gallet, B. / Lethier, M. / Bolla, J.M. / Pages, J.M. / Vivaudou, M. / Weik, M. / ...Authors: El-Khatib, M. / Nasrallah, C. / Lopes, J. / Tran, Q.T. / Tetreau, G. / Basbous, H. / Fenel, D. / Gallet, B. / Lethier, M. / Bolla, J.M. / Pages, J.M. / Vivaudou, M. / Weik, M. / Winterhalter, M. / Colletier, J.P.
#1: Journal: Plos One / Year: 2015
Title: Understanding Voltage Gating of Providencia Stuartii Porins at Atomic Level.
Authors: Song, W. / Bajaj, H. / Nasrallah, C. / Jiang, H. / Winterhalter, M. / Colletier, J. / Xu, Y.
History
DepositionNov 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PORIN 1
B: PORIN 1
C: PORIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,1444
Polymers117,1043
Non-polymers401
Water2,882160
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-44.9 kcal/mol
Surface area42160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.520, 142.020, 113.320
Angle α, β, γ (deg.)90.00, 131.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN C
211CHAIN A
311CHAIN B

-
Components

#1: Protein PORIN 1


Mass: 39034.527 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROVIDENCIA STUARTII (bacteria) / Plasmid: PG_OMP-PST1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): DELTA-OMP8 / References: UniProt: E3U904
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.8 % / Description: NONE
Crystal growpH: 6.5
Details: 14% PEG6000 MME, 0.1 M BUFFER MES PH6.5, 0.1 M MGCL2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 27279 / % possible obs: 90.5 % / Observed criterion σ(I): 2 / Redundancy: 2.68 % / Biso Wilson estimate: 53.11 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.98
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 2.66 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 93.2

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODELLER-MODEL OF OMP-PST1 BASED ON PDB ENTRY 1OPF

1opf


Resolution: 3.2→36.254 Å / SU ML: 0.99 / σ(F): 1.99 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2611 1364 5 %
Rwork0.2075 --
obs0.2102 27270 91.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 3.913 Å2 / ksol: 0.236 e/Å3
Displacement parametersBiso mean: 43.916 Å2
Baniso -1Baniso -2Baniso -3
1-9.412 Å20 Å219.1876 Å2
2---8.4621 Å20 Å2
3----0.9499 Å2
Refinement stepCycle: LAST / Resolution: 3.2→36.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8271 0 1 160 8432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068472
X-RAY DIFFRACTIONf_angle_d1.00711444
X-RAY DIFFRACTIONf_dihedral_angle_d15.2433022
X-RAY DIFFRACTIONf_chiral_restr0.0741158
X-RAY DIFFRACTIONf_plane_restr0.0041526
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C2721X-RAY DIFFRACTIONPOSITIONAL
12A2721X-RAY DIFFRACTIONPOSITIONAL0.051
13B2739X-RAY DIFFRACTIONPOSITIONAL0.045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.31430.3851390.30272657X-RAY DIFFRACTION93
3.3143-3.44690.31021390.2632636X-RAY DIFFRACTION93
3.4469-3.60360.31370.232597X-RAY DIFFRACTION92
3.6036-3.79340.30241360.20862591X-RAY DIFFRACTION92
3.7934-4.03080.25561380.19982622X-RAY DIFFRACTION92
4.0308-4.34160.24561370.18042605X-RAY DIFFRACTION92
4.3416-4.77760.22091360.15972567X-RAY DIFFRACTION91
4.7776-5.46690.21121360.16412596X-RAY DIFFRACTION91
5.4669-6.880.24651350.20282555X-RAY DIFFRACTION90
6.88-36.25650.24181310.22942480X-RAY DIFFRACTION86
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3834-0.48631.17171.651-0.1641.1927-0.02180.3802-0.059-0.1582-0.0338-0.0490.3962-0.10830.11630.6034-0.02530.00430.65040.01360.4441-22.565630.357211.3822
21.79560.2561.26581.14430.15972.0044-0.174-0.1833-0.27270.04790.0444-0.07410.5233-0.12710.15820.8639-0.00220.13320.64660.01130.6586-26.582512.899918.8737
31.6781-0.05190.22322.2821-0.76552.00150.2079-0.19390.10980.05180.07660.5937-0.0441-0.2232-0.26470.6549-0.122-0.0360.77-0.16790.5675-41.59720.60619.6254
42.0451-0.55010.79871.8130.03820.62370.0896-0.0050.20550.09020.12740.03850.06630.2323-0.18110.45010.0679-0.04960.7758-0.04790.4903-9.816938.294820.2448
51.4887-0.9282-0.25362.08710.28991.1162-0.1077-0.4488-0.00320.39080.1876-0.1390.05970.5792-0.09710.50320.0121-0.08521.00260.01150.5367-1.506341.233636.1315
62.57910.65531.77752.35230.61791.8256-0.1780.3448-0.154-0.48350.3064-0.4252-0.09450.8983-0.15250.5728-0.10710.12390.72920.02240.6894-22.078848.438711.8144
71.05050.44810.05951.982-0.32821.54660.2696-0.07560.39660.1923-0.13570.4134-0.2861-0.1872-0.08840.6580.02970.11270.58520.01590.7166-35.205860.116913.8386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:86)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 87:260)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 261:352)
4X-RAY DIFFRACTION4CHAIN C AND (RESSEQ 1:86)
5X-RAY DIFFRACTION5CHAIN C AND (RESSEQ 87:352)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 1:86)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 87:352)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more